5KF9

X-ray structure of a glucosamine N-Acetyltransferase from Clostridium acetobutylicum in complex with N-acetylglucosamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5KF1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82937-10% PEG-5000, 100 mM HEPPS, 5 mM CoA, 20 mM N-acetylglucosamine
Crystal Properties
Matthews coefficientSolvent content
2.1943.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.314α = 90
b = 44.607β = 120.9
c = 74.197γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2015-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9876APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.495099.30.0660.06648.44.853438
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.491.5599.80.3776.33.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5KF11.495050753264898.70.1760.1750.206RANDOM20.98
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.07-0.52.03-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39
r_dihedral_angle_4_deg17.249
r_dihedral_angle_3_deg14.63
r_long_range_B_refined6.592
r_long_range_B_other6.592
r_dihedral_angle_1_deg6.507
r_scangle_other5.516
r_scbond_it3.777
r_scbond_other3.774
r_mcangle_it3.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39
r_dihedral_angle_4_deg17.249
r_dihedral_angle_3_deg14.63
r_long_range_B_refined6.592
r_long_range_B_other6.592
r_dihedral_angle_1_deg6.507
r_scangle_other5.516
r_scbond_it3.777
r_scbond_other3.774
r_mcangle_it3.011
r_mcangle_other3.011
r_mcbond_it2.213
r_mcbond_other2.208
r_angle_refined_deg1.989
r_angle_other_deg0.881
r_chiral_restr0.3
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2620
Nucleic Acid Atoms
Solvent Atoms253
Heterogen Atoms117

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing